Emboss a logo in a complex mesh
Most of the time when your boolean its due to questionable topology. I am guessing you are using the boolean modifier at the moment but there is actually a better option. Select the logo then the mesh you want to emboss it in, then use the shortcut Ctrl - (minus), it'll make the logo transparent and can cut into the model much more cleanly. Once you are satisfied go to your 'modifier' tab on your mesh and apply the b_tool modifier. Good luck.